the aim of this research is to calculate the elastic constants and bulk modulus of cu-20 wt% ni random nanoalloy. the molecular dynamics simulation technique was used to calculate the mechanical properties in npt ensemble. the interaction between atoms as well as cohesive energy in the nanoalloy modeled systems was calculated by morse et al. two body potential. also the temperature of the syste...

the aim of this study is investigating the transport mechanism of ibuprofen chiral isomers inside singlewall carbon nano tube (swcnt) using mathematical modeling. to achieve this goal, molecular dynamicssimulation has been performed to evaluate the interactions of ibuprofen isomers with swcnt in an aqueoussolution. results show that both chiral forms of ibuprofen molecules enter and remain insi...

Molecular dynamics (MD) was widely used in chemistry and bio molecules. Numerous attempts have been made to accelerate MD simulations. CUDA enabled NVIDIA Graphics processing units (GPUs) use as a general purpose parallel computer chips as CPU. But it is not easy to port a program to GPU. We present a highly extensible framework for molecular dynamics simulation. And we discuss how to accelerat...

In this paper we present the results of utilizing scientific computing methodologies to address an engineering problem from nano technologies. In nano and micro­scale, the calculation could only be done with some particle based representation method. One of them is Molecular Dynamics (MD) method. In the paper we describe the construction of the Molecular Dynamics Method and ...

We consider tracer diffusion in colloidal suspensions under solid loading conditions, where hydrodynamic interactions play an important role. To this end, we carry out computer simulations based on the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) technique. Many details of the simulation method are discussed in detail. In particular, our choices for the SRD-MD parameters and ...

Background: Human serum albumin (HSA) is one of the most prominent protein in human blood. Trimethoprim (TMP) is an efficient antibiotic drug for treatment of pneumocystis pneumonia (PCP). Patients with HIV/AIDS and cancer are extremely affected by the disease due to immune system deficiency. Objective: The aim of this study is to evaluate the molecular dynamics simulation (MD) of HSA with TMP...

The molecular dynamics (MD) simulation method is used to assess structural details for humanprion protein (hereafter PrPN) and its Asp178 Asn mutant (hereafter PrPm) which causes fatalfamilial insomnia disease. The results reveal that the flexibility and instability increase in PrPmcould be related to specific amino acids exposed to the solvent. Solvation free energy of PrPm is 20kjmot1nni2 mor...

Different perturbation theories for the relative permittivity of dipolar model fluids are assessed by comparison to a comprehensive set molecular dynamics (MD) simulation data Stockmayer fluids. With exception dense liquids, all MD univariate function so-called dipole strength y. Overall, good agreement is found between some and data.

A molecular dynamics algorithm in principal component space is presented. It is demonstrated that sampling can be improved without changing the ensemble by assigning masses to the principal components proportional to the inverse square root of the eigenvalues. The setup of the simulation requires no prior knowledge of the system; a short initial MD simulation to extract the eigenvectors and eig...

A combined theoretical and molecular dynamics (MD) simulation study of the collective modes and their dispersion in a two-dimensional Yukawa system in the strongly coupled liquid state is presented. The theoretical analysis relies upon the quasilocalized charge approximation; the MD simulation generates static pair correlation functions and dynamical current-current correlation spectra.